Comments (7)
Hey, can try this with the env activated?
type -a mmseqs
from hecatomb.
Hey @beardymcjohnface yes sure:
$ conda activate miniconda/envs/hecatomb/snakemake/workflow/conda/897532ef0e68f9817d256b9cbd8a8111
$ type -a mmseqs
-bash: type: mmseqs: not found
from hecatomb.
That is really weird. I would try deleting the conda env and rerunning incase it was malformed.
rm -rf miniconda/envs/hecatomb/snakemake/workflow/conda/897532ef0e68f9817d256b9cbd8a8111
hecatomb run --test
If that still doesn't work, just see if you can get mmseqs installed at all as there might be some bioconda build issue for your system.
conda create -n testmmseqs -c conda-forge -c bioconda mmseqs2=12.113e3=h2d02072_2
conda activate testmmseqs
mmseqs --help
from hecatomb.
It's funny, I had tried to manually install mmseq2 using the same method you described in the fastp issue, but I get dependency errors.
Here's a gist because the console log is long: https://gist.github.com/alanorth/c916e218ab1fac9fd08fe25ea527e220
Note at the bottom the dreaded "strict channel priority" again.
from hecatomb.
What's your default channel priority? The mmseqs env should only have three bioconda deps and they're not in conda-forge, so you'd want conda-forge above bioconda. my hecatomb-mmseqs env:
$ conda list
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
ca-certificates 2022.5.18.1 ha878542_0 conda-forge
csvtk 0.23.0 h9ee0642_0 bioconda
gawk 5.1.0 h7f98852_0 conda-forge
gettext 0.19.8.1 h73d1719_1008 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 12.1.0 h8d9b700_16 conda-forge
libgomp 12.1.0 h8d9b700_16 conda-forge
libidn2 2.3.2 h7f98852_0 conda-forge
libstdcxx-ng 12.1.0 ha89aaad_16 conda-forge
libunistring 0.9.10 h7f98852_0 conda-forge
libzlib 1.2.12 h166bdaf_0 conda-forge
mmseqs2 12.113e3 h2d02072_2 bioconda
openssl 3.0.3 h166bdaf_0 conda-forge
taxonkit 0.8.0 h9ee0642_0 bioconda
wget 1.20.3 ha35d2d1_1 conda-forge
zlib 1.2.12 h166bdaf_0 conda-forge
this is my ~/.condarc
file:
channels:
- conda-forge
- bioconda
- defaults
channel_priority: strict
from hecatomb.
My ~/.condarc
didn't have any channels in it (I don't normally use Conda). After adding the channels, deleting the Conda env that hecatomb created for mmseq2 (some directory named with a long hash above), then re-running hecatomb run --test
it seems to be working.
Curious why the channel list in envs/hecatomb/snakemake/workflow/envs/mmseqs2.yaml
isn't good enough:
name: mmseqs2
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- mmseqs2=12.113e3=h2d02072_2
- taxonkit=0.8.0
- csvtk=0.23.0
from hecatomb.
I'm curious as well. I'll see if I can reproduce this weirdness on my system; it might be a snakemake or a conda issue.
from hecatomb.
Related Issues (20)
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